#load long-form module list as data frame
data <- read.csv("../Data/ClusterProfiler/modules-gene-long.csv", header = TRUE)
#filter to module
data.green <- data %>%
filter(module == "green")
data.black <- data %>%
filter(module == "black")
data.brown <- data %>%
filter(module == "brown")
data.yellow <- data %>%
filter(module == "yellow")
data.blue <- data %>%
filter(module == "blue")
data.red <- data %>%
filter(module == "red")
data.pink <- data %>%
filter(module == "pink")
data.magenta <- data %>%
filter(module == "magenta")
data.turquoise <- data %>%
filter(module == "turquoise")
#Extract only list of KOs
data.green <- data.green$KO
data.black <- data.black$KO
data.brown <- data.brown$KO
data.yellow <- data.yellow$KO
data.blue <- data.blue$KO
data.pink <- data.pink$KO
data.magenta <- data.magenta$KO
data.turquoise <- data.turquoise$KO
data.red <- data.red$KO
#KEGG pathway over-representation analysis
k.green <- enrichKEGG(gene = data.green,
organism = 'ko',
pvalueCutoff = 0.05)
## Reading KEGG annotation online:
##
## Reading KEGG annotation online:
k.black <- enrichKEGG(gene = data.black,
organism = 'ko',
pvalueCutoff = 0.05)
k.brown <- enrichKEGG(gene = data.brown,
organism = 'ko',
pvalueCutoff = 0.05)
k.yellow <- enrichKEGG(gene = data.yellow,
organism = 'ko',
pvalueCutoff = 0.05)
k.blue <- enrichKEGG(gene = data.blue,
organism = 'ko',
pvalueCutoff = 0.05)
k.red <- enrichKEGG(gene = data.red,
organism = 'ko',
pvalueCutoff = 0.05)
k.pink <- enrichKEGG(gene = data.pink,
organism = 'ko',
pvalueCutoff = 0.05)
k.magenta <- enrichKEGG(gene = data.magenta,
organism = 'ko',
pvalueCutoff = 0.05)
k.turquoise <- enrichKEGG(gene = data.turquoise,
organism = 'ko',
pvalueCutoff = 0.05)
#KEGG module over-representation analysis
m.green <- enrichMKEGG(gene = data.green,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
## Reading KEGG annotation online:
##
## Reading KEGG annotation online:
m.black <- enrichMKEGG(gene = data.black,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
m.brown <- enrichMKEGG(gene = data.brown,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
m.yellow <- enrichMKEGG(gene = data.yellow,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
m.blue <- enrichMKEGG(gene = data.blue,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
m.red <- enrichMKEGG(gene = data.red,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
m.pink <- enrichMKEGG(gene = data.pink,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
m.turquoise <- enrichMKEGG(gene = data.turquoise,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
m.magenta <- enrichMKEGG(gene = data.magenta,
organism = 'ko',
pvalueCutoff = 1,
qvalueCutoff = 1)
## wrong orderBy parameter; set to default `orderBy = "x"`
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## Warning: ggrepel: 19 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## Warning: ggrepel: 127 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## wrong orderBy parameter; set to default `orderBy = "x"`
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
### Network plots
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.